Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_051939905.1 BS73_RS13630 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000744815.1:WP_051939905.1 Length = 348 Score = 120 bits (302), Expect = 5e-32 Identities = 89/303 (29%), Positives = 139/303 (45%), Gaps = 34/303 (11%) Query: 92 RWAVLALVVVAFVWPFFA------------SRGAVDIATLILIYVMLGIGLNIVVGLAGL 139 RW L++V + P+ A S G + + L L++ L G ++++G GL Sbjct: 2 RWWPAPLLLVLLIAPYSAVPLPGLLDGPIGSAGNLQLIALCLVFGGLATGYDLLLGRTGL 61 Query: 140 LDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIV 199 L G+ ++A G Y +L AG F A + L +LG LR+ G ++V Sbjct: 62 LSFGHALYFATGTYVTDVLMLRAGLPFAAAAVLGLAAGVLLAAVLGSVSLRVTGIGFSMV 121 Query: 200 TLGFGEIIRILL-RNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNT 258 TL F + IL+ R+ TGG G+ + R P + GI + Sbjct: 122 TLAFAQAGSILVTRDPGGATGGEEGLAAPAD----------RMPAAL------IGIGHTA 165 Query: 259 NYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFT 318 + LY +AL V+L V+ L+R PIGR WE ++E+E+ LGL P KL+AF Sbjct: 166 D-----LYWIALAYVVLTFAVVQWLLRSPIGRVWEGIKENELRVEVLGLRPHGFKLAAFV 220 Query: 319 IGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE 378 + + A G + G TP++ T + +L +VVLGG GS+ G +L V+ + Sbjct: 221 LSGALAALGGVVYLLLTGGATPQTTTSDFTLSLLVMVVLGGSGSRWGPLLGGVLYTWADQ 280 Query: 379 MRG 381 G Sbjct: 281 RLG 283 Lambda K H 0.330 0.146 0.439 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 395 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 348 Length adjustment: 30 Effective length of query: 387 Effective length of database: 318 Effective search space: 123066 Effective search space used: 123066 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory